The analytical studies are presented which was aimed at searching optimal conditions for the separation and identification of ink dyes with the use of the PrinCE 550 CE electrophoresis system. The ultimate task was to establish the minimum sample amount which have to be taken from ink lines on paper to perform a valuable analysis for criminalistic purposes. Micellar Electrokinetic Capillary Chromatography (MEKC) mode was applied to separation of dyes. The examinations were carried out using the standard mixtures of Methyl Violet B, Victoria Blue B and Solvent Black 3, and the sample requirements was evaluated for a black ball-point pen ink extracted from paper. It was stated that the minimum number of micro-dots punched out from examined document was established to be as small as 4. It was also revealed that the identification parameters for components of inks can be migration time as well as ratio of peak areas of dye isomers.